5 Metazoan Complexity
165
Moreover, mice deficient for this gene have demonstrated an essential role for pax6
in the differentiation of glucagon-secreting alpha cells of the pancreas (St-Onge
et al. 1997). As an example of the remarkable conservation of gene structures in
Bilateria, the Platynereis pax6 gene contains an intron in the PAIRED domain at the
precise site where it is found in vertebrates (see Raible et al. 2005 and Fig. 5.5). This
intron is instrumental in the generation of two functionally divergent splice variants
in vertebrates, but is absent from the genomes of the ascidians Ciona and Phallusia,
and has therefore traditionally been assumed to be a vertebrate innovation (Callaerts
et al. 1997). The data from Platynereis suggest that the ancestral eubilaterian pax6
locus already possessed the necessary introns for generating alternative splice variants at this site. There is not yet any experimental evidence for the existence of
a specific splice variant in Platynereis. In keeping with this possibility, however,
the two sets of orthologues observed in Drosophila are mainly distinct in their
N-terminal portion, consistent with the fixation of ancestral splice variants in the fly
genome (Fig. 5.5). Moreover, vertebrate Pax6(5a) can substitute for the Drosophila
eyg gene (Dominguez et al. 2004), indicating a functional equivalence that has so far
been regarded as the product of parallel evolution. Notably, a recent report describes
the isolation of alternative splice variants in Amphioxus that are compatible with the
notion of an ancestral splice event in the PAIRED domain predating the evolution
of vertebrates (Short and Holland 2008).
5.10 Alternative Splicing: Modulating the Basic Layers
of Genomic Complexity?
Besides the specific example outlined above, the repeated finding of complex gene
structures at the base of animal evolution raises a more general question concerning
the evolution of transcriptome complexity and its relationship with animal complexity. From early genome measurements, as well as from the first whole-genome
projects, it became clear that neither genome size nor the number of proteincoding genes correlate well with the assumed morphological complexity of different
animals: complex metazoans can have smaller genomes than protozoans (c-value
paradox) and the total gene number in complex vertebrates is not fundamentally
higher than in invertebrates (the n- or g-value paradox) (Claverie 2001, Hahn and
Wray 2002). Alternative splicing provides a direct way to modulate the complexity
of a proteome irrespective of changes in gene number (reviewed in Maniatis and
Tasic 2002), and therefore is an attractive candidate for mediating cell type complexity. Whereas it is difficult to capture the full extent of alternative transcripts in
any organism, first global analyses at least indicate that even between closely related
species such as humans and chimpanzees, there are significant changes in the splicing of 6–8% of orthologous exons (Calarco et al. 2007). As this is a significant figure
compared to the few documented cases of gene gain/loss between the two species
(Chimpanzee Sequencing and Analysis 2005), this suggests that changes in alternative splicing could well contribute to changes in complexity between species, or
165
Moreover, mice deficient for this gene have demonstrated an essential role for pax6
in the differentiation of glucagon-secreting alpha cells of the pancreas (St-Onge
et al. 1997). As an example of the remarkable conservation of gene structures in
Bilateria, the Platynereis pax6 gene contains an intron in the PAIRED domain at the
precise site where it is found in vertebrates (see Raible et al. 2005 and Fig. 5.5). This
intron is instrumental in the generation of two functionally divergent splice variants
in vertebrates, but is absent from the genomes of the ascidians Ciona and Phallusia,
and has therefore traditionally been assumed to be a vertebrate innovation (Callaerts
et al. 1997). The data from Platynereis suggest that the ancestral eubilaterian pax6
locus already possessed the necessary introns for generating alternative splice variants at this site. There is not yet any experimental evidence for the existence of
a specific splice variant in Platynereis. In keeping with this possibility, however,
the two sets of orthologues observed in Drosophila are mainly distinct in their
N-terminal portion, consistent with the fixation of ancestral splice variants in the fly
genome (Fig. 5.5). Moreover, vertebrate Pax6(5a) can substitute for the Drosophila
eyg gene (Dominguez et al. 2004), indicating a functional equivalence that has so far
been regarded as the product of parallel evolution. Notably, a recent report describes
the isolation of alternative splice variants in Amphioxus that are compatible with the
notion of an ancestral splice event in the PAIRED domain predating the evolution
of vertebrates (Short and Holland 2008).
5.10 Alternative Splicing: Modulating the Basic Layers
of Genomic Complexity?
Besides the specific example outlined above, the repeated finding of complex gene
structures at the base of animal evolution raises a more general question concerning
the evolution of transcriptome complexity and its relationship with animal complexity. From early genome measurements, as well as from the first whole-genome
projects, it became clear that neither genome size nor the number of proteincoding genes correlate well with the assumed morphological complexity of different
animals: complex metazoans can have smaller genomes than protozoans (c-value
paradox) and the total gene number in complex vertebrates is not fundamentally
higher than in invertebrates (the n- or g-value paradox) (Claverie 2001, Hahn and
Wray 2002). Alternative splicing provides a direct way to modulate the complexity
of a proteome irrespective of changes in gene number (reviewed in Maniatis and
Tasic 2002), and therefore is an attractive candidate for mediating cell type complexity. Whereas it is difficult to capture the full extent of alternative transcripts in
any organism, first global analyses at least indicate that even between closely related
species such as humans and chimpanzees, there are significant changes in the splicing of 6–8% of orthologous exons (Calarco et al. 2007). As this is a significant figure
compared to the few documented cases of gene gain/loss between the two species
(Chimpanzee Sequencing and Analysis 2005), this suggests that changes in alternative splicing could well contribute to changes in complexity between species, or